when i try to configure pop3 and IMAP setting for the newdomain .. i am able to download mails from existingdomain only .

What do you think a Virtual Domain would allow you to do anything else? This is a quote from the help text above the Virtual Domain box in the Admin UI:

Virtual hosts allow the system to establish a default domain for a user login. Any user that logs in while using a URL with one of the hostnames below will be assumed to be in this domain, 'yourdomain.com' . Please note, that removal of a virtual host takes effect only after mailbox server is restarted.

You have not added an additional domain to your server, you've added a Virtual Domain that points to your existing domain and therefore you will see the mail in that domain users mailbox.

If you wanted different domains you need to add them as a new domain and create new mailboxes on those domains. What are you trying to do with this set-up?

Hi Phoneix ,
yeah , I have created separate domain in Admin UI . I have created seperate user as you have mentioned earlier for the new domain .

I have seen logs of /var/log/zimbra.log , /var/log/maillog and i didnt trace any error in this logs ...

So what are you telling me now? If you have a separate domain with users then they can use any client to get the email from thos accounts, there is no problem doing that, if that's what you're doing and it appears not to be working then you need to give an exact description of what happens on the client when they connect and what you see in the log files (including some information from the audit log that the have connected).